Cubik2k thanks for the reply. There is no proto that I could set read only to begin with. After an uninstall and clean install of fo2 and mapper I have the exact same issue. I'll brake down everything so that anyone interested can help me out.
Fo2 dir: F:\Games\Retro\Fallout2
(removed any read only attributes from the \data folder, subfolders and files in it;
check out for items.lst, it's there and it's populated;
renam patch000.dat to patch000.bak)
Mapper dir: F:\Fallout 2 Mapper
(set librarian=1, set paths critter_dat=F:\Games\Retro\Fallout2\critter.dat
critter_patches=F:\fallout2\dev\data
master_dat=F:\Games\Retro\Fallout2\master.dat
master_patches=F:\fallout2\dev\data)
Extra dirs: F:\fallout2\dev\data\proto\items
\critters, \misc, \scenery, \tiles, \walls
What happens: load the mapper, go at the empty box after frank's gun, edit, make a new weapon, hit done, no errors, exit mapper
Check out F:\fallout2\dev\data\proto\items, there's items.lst with one entry 00000532.pro (nothing else)
Check out F:\Games\Retro\Fallout2\data\Proto\Items, there's items.lst (it was there before), with all the .dat entries, no new entries (no 532 in it).
Load mapper, now it reads the items.lst from the patch dir, so no items show up.
Close mapper, delete items.list from patch dir, load mapper, try to edit an existing weapon, can't save error.
Extract a random weapon proto and put it in fo2 \items dir, try to edit it, can't save error.
Take that weap proto, put it in patch \items dir, create a new items.lst with the relevant pro entry, mapper loads only that weap in items, try to edit it, can't save error.
No file or dir whatsoever has the read only attribute and I have changed the security settings of the aforementioned dirs, so they can be edited from all the user groups (even though I log in an admin account).
I'm completely baffled.